This study was undertaken to determine the factors that influence the output of aquaculture production and the profitability of three production systems (concrete tank, earthen pond, and mobile tank) in Southern Agricultural Zone of Cross River State. A multi-stage stratified random sampling technique was used to select 140 farmers from three LGAs in the study area. Structured questionnaire was used for data acquisition. Descriptive and inferential statistics alongside budgeting techniques were used in data analysis. ANOVA results indicates that there was significant difference (P<.01) among the mean output of fish per pond from the three production systems, with earthen pond having the highest value (2163.65), followed by concrete tank (1515.77), and mobile tank (263.05). The mean values of the gross margins in the three production systems indicated that earthen pond had highest values (₦1,138,682.35), followed by concrete tank (₦935,326.18)), and mobile tank (₦792,385.00). Years of experience, quantity of feed, stocking density and labour had positive influences on output for concrete tank, while quantity of feed, labour and years of experience had positive and significant influence on output for earthen pond. Educational level and quantity of feed had positive and significance influences on mobile tank output. The profitability ratios; return on investment and return on sales indicate that there was no significant difference (P>.01) among the fish farming systems. Establishment of fish farm estates in the study area to enable fish farmers operate in clusters for efficient utilization of government facilities for enhanced productivity is recommended.