Three basin-fill hydrogeologic units comprise the aquifer system in the Yucaipa subbasin. Underlying these basin-filling units is crystalline basement, which likely has a continuous, thin layer of weathered saprolitic material along its upper surface. The three basin-fill hydrogeologic units (from oldest [deepest] to youngest [most shallow]) are referred to as (1) consolidated sedimentary materials, (2) unconsolidated sediment, and (3) surficial materials. Consolidated sedimentary materials are more compacted, cemented, and have a greater abundance of clay and silt relative to the overlying unconsolidated sediment and surficial materials, making this unit the least permeable of the three. The unconsolidated sediment represents the primary aquifer unit, with more coarse- than fine-grained material and indicating a likelihood of high permeability and capacity for groundwater flow and storage. The surficial materials consist of unconsolidated, coarse-grained materials, and this unit is generally located above the water-table; therefore, this unit is unlikely to contribute to groundwater storage but permits rapid recharge to the groundwater table. Crystalline basement is the basal unit in the Yucaipa subbasin but should not be considered hydrologically impermeable. These rocks do not host large volumes of groundwater, but small-scale joints and fractures can serve as conduits to groundwater flow, and the presence of weathered saprolitic material may affect groundwater flow through the aquifer.

A series of faults and groundwater barriers dissect and bound the Yucaipa subbasin. These faults and barriers delineate 12 groundwater subareas (hereafter referred to as “subareas”), 7 of which comprise the majority of the aquifer system. Several faults and barriers have been shown or interpreted to inhibit groundwater flow (such as the Chicken Hill fault, Yucaipa graben complex, and the Cherry Valley thrust fault), as have geologic structures such as the folds associated with the Miocene Banning fault and the South Mesa barrier.

Present-day recharge to the basin-fill aquifer occurs primarily as deep percolation of mountain-front runoff and infiltration of streamflow in the Oak Glen, Triple Falls Creek, and Wilson Creek subareas in the northeastern part of the Yucaipa subbasin. Underflow from crystalline basement and infiltration from precipitation are additional sources of natural recharge to the basin-fill aquifer. Estimates of historical annual recharge in the Yucaipa subbasin generally range from about 7,000 acre-feet per year (acre-ft/yr) to more than about 13,000 acre-ft/yr. Water from northern California has been imported to the Yucaipa subbasin since 2002, has been applied directly as managed aquifer recharge (MAR) to the Wilson Creek and Oak Glen Creek spreading basins, and has been treated and used to augment the municipal water supply and reduce the demand for groundwater pumping. Between 2002 and 2014, about 69,200 acre-feet (acre-ft) of water was imported to the subbasin; about 17,900 acre-ft of this amount was applied as MAR. Pumpage estimates during 1947–2014 ranged from about 4,000 acre-ft in 1947 to a high of about 18,500 acre-ft in 2002. The average annual amount of groundwater removed from the Yucaipa subbasin by pumping during 1947–2014 was estimated to be about 12,800 acre-ft/yr, which was greater than most estimates of annual recharge to the subbasin.

The predominant direction of groundwater flow under historical and present-day conditions was from the northeastern subareas adjacent to the San Bernardino Mountains and the low hills just east of the City of Yucaipa (hereafter referred to as “Yucaipa hills”), to the west and south toward San Timoteo Creek, and eventually toward the Santa Ana River west of the subbasin. Natural discharge of deep groundwater occurs as evapotranspiration, and subsurface outflow along the western margin of the Yucaipa subbasin to the adjacent San Bernardino subbasin. Estimates of subsurface outflow across the western margin ranged from about 3,500 to 20,000 acre-ft/yr during 1905–2015; there was an overall decline in the estimated outflow values during this time, likely attributed to a steady decline in groundwater levels caused by pumping. The long-term extraction of groundwater has caused groundwater levels to decrease by nearly 200 feet (ft) since the 1940s in parts of the Calimesa and Western Heights subareas. Groundwater levels in subareas near the areas of natural recharge (such as the Oak Glen, Wilson Creek, and Crafton subareas) have declined by much less, and in some cases increased due to the application of MAR and reduction in pumping associated with the importation of water from northern California.

Four groundwater types were identified in the Yucaipa subbasin, the chemical character of which varied depending on the source and location of recharge. Most groundwater in the Yucaipa subbasin was calcium-bicarbonate-type water and was locally recharged from deep percolation of mountain-front runoff, streamflow, and precipitation. Groundwater recharged to the basin-fill aquifer through crystalline basement was sodium-sulfate-type water and was identified in deep wells in the Calimesa subarea; samples of this groundwater type did not have detectable tritium, indicating pre-modern recharge age. Groundwater in a perched aquifer in the Western Heights subarea was sulfate-rich, calcium-bicarbonate-type water. Water imported from northern California and applied as MAR in the Wilson Creek subarea was chloride-type water. At least some samples of all groundwater types, with the exception of water recharged through crystalline basement, had detectable tritium, indicating that most groundwater types had modern recharge ages. Concentrations of total dissolved solids (TDS) of groundwater ranged from about 225 to 1,120 milligrams per liter; groundwater samples with lower TDS concentrations generally were from wells near sources of natural recharge, and samples with the highest TDS concentrations were from deep wells near the contact with the crystalline basement rocks.

The YIHM is needed to better understand and quantify the hydrologic system of the Yucaipa subbasin and to quantify the effects of historical and potential water-resource development induced by climate changes and human-related activities, respectively. The YIHM was developed using the USGS Groundwater and Surface-water FLOW model (GSFLOW). GSFLOW simulation software consists of two integrated model components: (1) a watershed-component model developed by using Precipitation Runoff Modeling System (PRMS) and (2) a groundwater-component model developed by using MODFLOW-NWT. The integrated surface-water and groundwater model was developed for the YVW, a 121-mi² watershed that encompasses the Yucaipa subbasin.

The watershed-component of the YIHM was developed using the PRMS and performs a continuous daily simulation of the hydrologic processes of the land surface (including vegetation cover, soil-zone, and impervious and pervious areas). The watershed-component of the YIHM model included 14,012 hydrologic response units (HRUs) discretized to match the 492 ft on a side, grid-cell layout of the underlying groundwater-component model. The land surface HRUs are used to represent the spatial variability of land-surface elevation, slope, and aspect; vegetation type and cover; land use; distribution of precipitation, temperature, and solar radiation; soil morphology and geology; and flow direction. The HRUs were connected to a flow drainage network that routes surface water to one location of outflow on western portion of San Timoteo Creek near the City of Redlands. The daily climate input used in the YIHM was distributed from climate stations to all HRUs to account for spatial variability of precipitation and air temperature.

The groundwater-component model simulates water flow and storage in the unsaturated zone, the saturated zone, and the stream network. The groundwater-component model characteristics included a finite-difference grid of 134 rows and 237 columns with uniform, square model cells with a dimension of about 492 ft on each side. There were four layers of variable thickness. Aquifer properties were spatially defined by hydrogeologic units on the basis of previously published geology and borehole texture data. Boundary conditions included no-flow and head-dependent flow boundaries to allow for subsurface flow into or out of the YVW, as appropriate. A network of faults was simulated in the model as partial barriers to groundwater flow. The Yucaipa subbasin was divided into 12 subareas to aid in the analysis of groundwater budget conditions. Groundwater inflow included recharge (resulting from deep percolation of precipitation and return flow) through the unsaturated to saturated zone, recharge from streams, and subsurface flow from adjacent groundwater basins. Groundwater outflow included pumpage, base flow, groundwater evapotranspiration, surface leakage, and subsurface flow to adjacent groundwater basins and subbasins.

The YIHM was calibrated by using an Ensemble Smoother, Parameter Estimation software (PEST), and an iterative trial-and-error approach of adjusting model parameters to achieve a reasonable fit between simulated and measured solar radiation, potential evapotranspiration, average streamflow, and transient groundwater levels during the period 1970–2014. The calibration process for the YIHM included adjusting the initial estimates of the land-surface properties, soil-zone properties, stream-channel properties, aquifer properties, general-head boundary properties, and fault characteristics.

The YIHM was used to simulate the daily water budget for a continuous 67-year period that began January 1, 1947, and ended December 31, 2014. The calibrated YIHM was used to derive components of the daily water budgets for the components of the integrated model for calendar years 1970–2014 (long-term average), with particular attention given to groundwater budgets for dry and wet periods. The YIHM also was used to assess the effects of pumping and climate stresses on hydrologic-budget components in 12 subareas within the Yucaipa subbasin.