Hard clam aquaculture plays an important role in the U.S. shellfish industry, contributing 47.3% of clam aquaculture sales and 18.3% of the total mollusk industry. In Florida, most hard clam production occurs along the Gulf of Mexico, where 300 hectares of coastal mudflats are leased for shellfish farming. However, the industry faces increasing threats from rising water temperatures, low salinity, and harmful algal blooms (HABs). Using a stochastic bioeconomic model, we assess how these threats impact the profitability of Florida's clam aquaculture. High temperature and low salinity restrict clam development and increase mortality, reducing profitability. During HAB events, algae toxins accumulate in clams, making them unsafe to eat. Consequently, authorities close harvesting areas until conditions improve, causing losses and risking clams exceeding marketable size. The impacts vary by county: low salinity primarily affects northern counties like Franklin, decreasing the net present value (NPV) of the profit by 98.0%. Southern counties, particularly Charlotte, experience a 100.2% reduction in NPV due to high temperatures and HABs. Levy and Franklin Counties, which produce 88.0% of the region's clams, are particularly affected. Our findings enlighten local producers and policymakers on how present and future environmental challenges might influence Florida clam aquaculture profitability.