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Abstract Multiple-use conflicts of the marine benthos (“bottom-use conflicts”) are increasing as humans expand use of the coastal zone. These conflicts necessitate balanced policies that consider the economic and ecological benefits of different bottom uses. In the Virginia coastal lagoons on the US east coast, there is a potential bottom-use conflict between hard clam (Mercenaria mercenaria) aquaculture and seagrass (Zostera marina) meadows. We leveraged two decades (2001–2021) of aerial imagery and environmental data to quantify historic trends in bottom use, assess the realized niche of seagrass and clam aquaculture across depth, sand fraction, root mean square (RMS) velocity, fetch, and sea surface temperature (SST) anomaly, and used random forest models to predict the potential extent of seagrass, clam aquaculture, and bottom-use conflict. We found growth in the coverage of both seagrass (+ 3373%) and clam aquaculture (+ 140%) over the past 20 years with a corresponding increase in bottom-use conflict (+ 2579%), though conflict area remained relatively minor. Seagrass occurred in deeper areas with higher fetch, a higher frequency of SST anomalies, lower sand fraction, and similar RMS velocities to areas containing clam aquaculture. Our random forest models predicted potential for the expansion of seagrass (+ 62%) and clam aquaculture (+ 263.9%) with a relatively small area of predicted spatial overlap (12.3%) under current conditions. These results illustrate how species distribution models can help us understand the spatial impacts of aquaculture on natural ecosystems and inform managers and policy makers to create objective policies that balance socioeconomic and ecologic needs.