How anticipated climate change might affect long-term outcomes of present-day agricultural conservation practices remains a key uncertainty that could benefit water quality and biodiversity conservation planning. To explore this issue, we forecasted how the stream fish communities in the Western Lake Erie Basin (WLEB) would respond to increasing amounts of agricultural conservation practice (ACP) implementation under two IPCC future greenhouse gas emission scenarios (RCP4.5: moderate reductions; RCP8.5: business-as-usual conditions) during 2020-2065. We used output from 19 General Circulation Models to drive linked agricultural land use (APEX), watershed hydrology (SWAT), and stream fish distribution (boosted regression tree) models, subsequently analyzing how projected changes in habitat would influence fish community composition and functional trait diversity. Our models predicted both positive and negative effects of climate change and ACP implementation on WLEB stream fishes. For most species, climate and ACPs influenced species in the same direction, with climate effects outweighing those of ACP implementation. Functional trait analysis helped clarify the varied responses among species, indicating that more extreme climate change would reduce available habitat for large-bodied, cool-water species with equilibrium life-histories, many of which also are of importance to recreational fishing (e.g., northern pike, smallmouth bass). By contrast, available habitat for warm-water, benthic species with more periodic or opportunistic life-histories (e.g., northern hogsucker, greater redhorse, greenside darter) was predicted to increase. Further, ACP implementation was projected to hasten these shifts, suggesting that efforts to improve water quality could come with costs to other ecosystem services (e.g., recreational fishing opportunities). Collectively, our findings demonstrate the need to consider biological outcomes when developing strategies to mitigate water quality impairment and highlight the value of physical-biological modeling approaches to agricultural and biological conservation planning in a changing climate.