Coral reefs provide immense ecosystem and economic value, supporting biodiversity, fisheries, tourism, and coastal protection worth billions annually. However, widespread degradation from thermal stress, storms, disease, and human impacts has caused significant coral cover and reef structure loss, increasing coastal vulnerability and economic risks. While coral loss is well-documented, degradation of underlying reef infrastructure and surrounding seafloor changes remain poorly understood. This study addresses this knowledge gap by quantifying seafloor elevation and volume changes across 234.2 km² of the Upper Florida Keys (UFK) reef tract using historical bathymetric and modern lidar (light detection and ranging) data collected from two periods with distinctly different disturbance regimes: 1935–2002 (frequent storms and major coral loss) and 2002–2016 (few storms and persistently low coral cover). Analysis of over 25,000 data points revealed substantial elevation and volume loss during 1935–2002 (−0.1 ± 0.8 m; 13.6 × 10⁶ m³ net loss), shifting to minimal gains by 2002–2016 (0.0 ± 0.3 m; 1.6 × 10⁶ m³ net gain). Despite this shift, benthic cover data showed continued declines in stony coral, with increases in macroalgae and octocorals, indicating that limited reef accretion persists even with reduced storm activity. Spatial analyses highlighted variable accretion and erosion patterns across habitats and subregions, underscoring the limitations of localized measurements for ecosystem-wide assessments. Our findings demonstrate the value of integrating historical and modern datasets for regional reef monitoring, establishing baselines for restoration planning, and emphasizing the need for continued high-resolution monitoring to guide adaptive management amid ongoing environmental change.