The estimation of the carrying capacity (CC) is a fundamental process in integrated environmental management, policy making, and decision making. Aquaculture carrying capacity has been studied since the 1960s to allow estimation of the production limits of aquaculture projects and, hence, their maximum economic performance within sustainable limits for the local environment. One major drawback of these approaches is that they can provide CC estimates after a fish farm is installed and operates in a certain location (ex post approaches). This paper approaches the estimation of CC using a Bayesian/CHAID model of profiling information on the environmental quality, geomorphology, and human activities on the adjacent coastal area (land side) using as an indicator the trophic state of the marine area in terms of chlorophyll-a concentration (upper mesotrophic). This way, having the above information for a certain site, it is possible to calculate the maximum annual production of a cage fish farm so that the trophic state of the area will not exceed the environmental goal of the upper mesotrophic level. We examined the effects of 27 different physical, chemical, social and geomorphological parameters on CC (in fish biomass terms). CC was found to be correlated by particulate nitrogen (PN), silicates (Si-SiO4), salinity, and suspended particulate matter (SPM). The overall relationship found is: Biomassat CC level = +473.762[Chl-a] − 6856.64[PN] + 9.302[Salinity] − 473.5[Si-SiO4] + 341.864[SPM] − 207.046. The analysis performed allowed us to estimate the maximum levels for each factor to maintain a eutrophication status up to the upper mesotrophic level: particulate nitrogen < 0.018 mg/L, silicates < 0.137 mg/L, salinity > 38 PSU and SPM > 0.815 mg/L. Finally, the current fish farm licensing legislation in Greece concerning the CC estimation algorithm is discussed.