Emerging insects from freshwater ecosystems can be key prey to riparian predators, but research on these cross-ecosystem subsidies has typically focused on biomass fluxes rather than on nutritional aspects. Omega-3 long-chain polyunsaturated fatty acids (ω3 LC-PUFAs) synthesized by microalgae are rare in the terrestrial environment but critical to consumer growth, immune function, and reproduction. Here, we reviewed drought impacts on the production and transfer of ω3 LC-PUFAs from riverine to terrestrial ecosystems. Putative mechanisms include reductions in surface water and habitat connectivity, shifts in algal communities toward LC-PUFA-poor taxa (e.g. cyanobacteria rather than diatoms), shortened hydroperiods that constrain aquatic insect life cycles, and altered emergence phenology that may decouple timing of subsidies from riparian consumer demand. To explore these mechanisms, we conducted a pilot study comparing ω3 LC-PUFA profiles of aquatic insects from temporary and perennial streams in Pinnacles National Park, CA. Fatty acid profiles differed significantly among insect taxa and between hydrology types, although ω3 LC-PUFA concentrations at the community level did not differ between temporary and perennial streams. We then compared 2 abundant taxa that differ in life histories: water striders Aquarius sp. (Gerridae), short-lived insects that survive drought by migrating to wet habitat (i.e., resilient strategist); and fishflies Neohermes sp. (Corydalidae), long-lived insects that survive drought locally via physiological and life-history adaptations, by entering a dormant stage (i.e., resistance strategist). We found significant effects of hydrology on ω3 LC-PUFA concentrations in drought-adapted Neohermes, with concentrations in temporary sites increasing with insect body mass. Because compound-specific stable isotopes suggest Neohermes did not change diet with intermittency or body size, we propose that these insects bioaccumulate ω3 LC-PUFA over the repeated dormancy-growth cycles - becoming very rich in ω3 prior to metamorphosis. These results highlight the complexity of interpreting fatty acid data, and the importance of natural history (e.g., resilient v.s. resistant strategies) in influencing fatty acid profiles and responses to environmental variation. We contend that intensifying droughts may alter the amount and form of ω3 fatty acids transferred to the riparian environment, ‘silently’ disrupting a key linkage between rivers and their watersheds.