We use the Aquaculture Performance Indicators (APIs) methodology to collect data for three aquaculture production systems in Chile, and we also provide a framework to evaluate to what extent the input dimensions explain the outputs using a production function approach. Our analysis considers the production of mussels, algae, and northern scallops. We measured all API categories (outcomes and input metrics) and then grouped the metrics into different dimensions suitable for analysis. We compared the results for each production system and tested the equality of matched pairs of observations. Then, we evaluate the performance of the three production systems using the frame of a separable multiproduct production function. We found statistically significant differences in the aggregated performance and inputs between mussels and algae and mussels and northern scallops. However, we did not find statistical differences in the outputs. The results suggest that mussel production has a higher (average) level of sustainable inputs than the other production systems. This difference in inputs, however, is not fully reflected in output differences. While this is a first step, a larger data set with more aquaculture systems would better be a more fruitful application of this approach, and this is left for future research.