Abstract: Reducing carbon emissions and enhancing carbon sinks are central to China’s ecological civilization and high-quality development. Fisheries play a dual role in carbon dynamics: aquaculture inputs, energy use, and facility operations generate emissions, whereas aquatic organisms and water bodies provide carbon sink potential through biomass accumulation and carbon burial. In lake-intensive inland regions such as Huzhou City, freshwater fisheries are important for food security and rural development, but their city-scale carbon balance and low-carbon pathways remain insufficiently quantified. This study quantitatively assesses the carbon emissions, carbon sinks, and net carbon balance of Huzhou’s fisheries and explores feasible pathways for emission reduction and sink enhancement. A city-level fishery carbon accounting framework was constructed using fisheries yearbooks, local government reports, and relevant literature. Emissions were estimated from energy consumption, material inputs, and production processes related to aquaculture and associated activities, while carbon sinks were calculated mainly from the biomass accumulation of aquaculture species, including fish, crustaceans, and shellfish, using established carbon conversion coefficients. Recent years were analyzed, with 2023 used as the representative period. Results show that in 2023, Huzhou’s fishery carbon sink was approximately 2.95×10⁵ t, while carbon emissions reached 9.81×10⁵ t, resulting in a net carbon emission of about 6.86×10⁵ t. The sector therefore remains a net carbon source, and short-term net carbon balance is unlikely. Freshwater fish and crustaceans dominated both sinks and emissions, reflecting the local aquaculture structure. Over time, carbon sinks increased due to output expansion and species optimization, whereas emissions remained relatively stable. Efficiency improvement, feed optimization, and ecological aquaculture models are key measures for strengthening sink capacity and reducing emissions. Considering industrial realities, tailored targets for carbon reduction and sink enhancement in Huzhou’s fisheries are proposed: a carbon emission peak by 2030, with an estimated peak value of 1.3×10⁶−1.4×10⁶ t, and a subsequent net carbon balance target aiming to reduce net emissions to approximately 6×10⁵−7×10⁵ t. To achieve these goals, eight major technological pathways are proposed from the perspectives of carbon reduction, pollution control, green expansion, and sink enhancement: optimizing aquaculture product structure, promoting integrated rice–fish farming, developing multi-trophic aquaculture systems, expanding ecological aquaculture in large water bodies, strengthening aquaculture tailwater pollution treatment, replacing conventional aquaculture energy with cleaner energy, advancing smart fishery technologies, and promoting recirculating aquaculture systems. This study provides quantitative evidence of the current net carbon source status of Huzhou's fisheries and highlights the structural and technological factors influencing carbon balance. The proposed pathways offer practical guidance for local policymakers and stakeholders in formulating low-carbon strategies. These findings provide quantitative evidence of the net carbon source status of Huzhou’s fisheries and offer practical guidance for local low-carbon fishery strategies and similar lake-based regions pursuing sustainable development.