With the recent trends in urban agriculture and climate change, there is an emerging need for alternative plant culture techniques where dependence on soil can be eliminated. Hydroponic and aquaponic growth techniques have proven to be viable alternatives, but the lack of efficient and optimal practices for irrigation and nutrient supply limits its applications on a large-scale commercial basis. The main purpose of this research was to develop statistical methods and Machine Learning algorithms to regulate nutrient concentrations in aquaponic irrigation water based on plant needs, for achieving optimal plant growth and promoting broader adoption of aquaponic culture on a commercial scale. One of the key challenges to developing these algorithms is the sparsity of data which requires the use of Bolstered error estimation approaches. In this paper, several linear and non-linear algorithms trained on relatively small datasets using Bolstered error estimation techniques were evaluated, for selecting the best method in making decisions regarding the regulation of nutrients in hydroponic environments. After repeated tests on the dataset, it was decided that Semi-Bolstered Resubstitution Error estimation technique works best in our case using Linear Support Vector Machine as the classifier with the value of penalty parameter set to one. A set of recommended rules have been prescribed as a Decision Support System, using the output of the Machine Learning algorithm, which have been tested against the results of the baseline model. Further, the positive impact of the recommended nutrient concentrationson plant growth in aquaponic environments has been elaborately discussed. •This study presents a ML based technique for nutrient regulation in coupled aquaponics system.•The performance of linear and non-linear classifiers on small datasets has been studied.•Bolstered error estimate strategies instead of MSE techniques have been prescribed.•The idea of inferencing in data-depleted domains has been addressed.•ML-based recommendations to optimize nutrients have been implemented against baseline model.