Abstract Within the framework of Ecosystem Approach to Aquaculture (EAA), ecological carrying capacity (ECC) is a key concept that helps to determine the upper limit of production without compromising ecosystem functioning. The implementation of ECC is complex as ECC differs between type of farms and location and standardised methods should be developed for management. There is therefore a clear need for operational indicators. The objectives of this paper were: (1) to carry out a systematic literature review on shellfish and seaweed aquaculture‐environment interactions to list the most used environmental indicators, (2) to classify the indicators according to the effects they measure (i.e., benthic, water quality, food web interactions, cultured organism health, resource use) and the scale at which they are applied, and (3) to assess their potential based on four indicator criteria categories: sensitivity, accuracy and precision, feasibility and utility, and ecosystem‐level scalability. Overall, indicators describing benthic effects were the most highly cited and scored. Indicators identified for bivalve and seaweed culture were discussed and compared to previous work on salmon aquaculture indicators to highlight similarities and differences across trophic levels. In addition, questions related to the challenges of ECC indicators implementation were presented to a panel of experts. The scoring and consultation provided the source of discussion on environmental management consistent with EAA.