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In light of ongoing trends in metropolitan farming and global climate shifts, there is a growing need for alternative plant cultivation strategies that can operate independently of soil. Aquaponic and hydroponic growing methods have proven workable replacements, yet the scarcity of streamlined, ideal procedures for watering and nutrient delivery curtails their deployment at a mass commercial scale. The primary objective of this investigation was to develop statistical techniques and Machine Learning models to adjust nutrient levels in aquaponic irrigation systems in response to crop demand, thereby securing peak plant performance and facilitating wider commercial uptake of aquaponic farming. A core difficulty in crafting these models is the thinness of available data, which calls for the application of Bolstered error estimation methodologies. This paper assesses a range of linear and non-linear algorithms conditioned on comparatively small data sets using bolstered error estimation techniques to identify the superior approach for guiding nutrient control decisions in hydroponic contexts. Upon conducting multiple tests on the data, it was concluded that the Semi-Bolstered Resubstitution Error estimation strategy yields the best results in our scenario, using a Linear Support Vector Machine as the categorizer with a penalty factor of 1. A series of suggested directives was developed as a Decision Support System, derived from the Machine Learning model’s outputs, and verified against the baseline framework’s findings. Moreover, the constructive influence of the recommended nutrient mixtures on plant growth in aquaponic conditions is examined in detail.