Invertebrates, such as brine shrimp and brine flies, are key prey items for millions of resident and migratory birds that utilize saline lakes such as Great Salt Lake (GSL). Elevated methylmercury (MeHg) in invertebrate and waterfowl species of GSL has been assumed to be linked to elevated MeHg in GSL’s anoxic Deep Brine Layer (DBL) where aqueous concentrations can exceed 30 ng/L. Here, we leverage mercury (Hg) concentration and stable isotope measurements on brine flies (Ephydra hians and Ephydra cinerea), brine shrimp (Artemia franciscana), and spider (western spotted orbweaver [Neoscona oaxacensis]) to examine temporal changes in Hg concentrations and sources during periods of DBL presence and absence. Mercury concentrations in brine flies were inversely correlated with lake level and directly correlated with salinity, possibly resulting from factors such as enhanced Hg bioaccumulation due to osmoregulatory stress and stunted growth and/or elevated salinities impacting composition, abundance, and Hg concentrations of food sources. DBL presence did not correspond to higher invertebrate Hg concentrations, highlighting that the DBL is not the primary source of MeHg to biota. Hg stable isotope signatures (Δ¹⁹⁹Hg and δ²⁰²Hg) in brine shrimp varied seasonally and indicated greater cumulative photochemical Hg loss from the water column in late summer and fall months. Co-located brine fly and western spotted orbweaver samples show equivalent Δ¹⁹⁹Hg and δ²⁰²Hg signatures, supporting Hg transfer from the aquatic to terrestrial food webs. Furthermore, Hg isotope results (Δ²⁰⁰Hg) indicate that the majority of Hg accumulating in GSL invertebrates is of atmospheric origin. This study highlights temporal controls on Hg bioaccumulation within GSL, which will help assess Hg cycling within the system in response to management actions and declining lake levels.