Floating photovoltaic (FPV) systems are a novelty of interest in Poland due to the demand for increasing the share of renewable energy sources in electricity generation. Due to the novelty of FPV systems, insufficient maturity, and limited research available, FPV systems are an area requiring intensive research to evaluate their potential as a competitive solution to classical ground-mounted photovoltaic systems (GMPV). The evaluation of FPVs involves multiple indicators comprising aspects such as cost-effectiveness from an economic point of view and technical performance. This suggests the usefulness of multi-criteria analysis in their evaluation. However, the choice of method should take into account aspects such as sustainability and decision-maker preferences in addition to the multi-criteria analysis. The aim of this paper is to introduce the Strong Sustainability Paradigm based Technique for Order Preference by Similarity to Ideal Solution (SSP-TOPSIS) method for modeling the degree of compensation reduction of criteria according to the strong sustainability paradigm. The method was applied to the practical multi-criteria problem of evaluating FPV systems against a reference GMPV system taking into account technical and economic aspects. A modification of the level of compensation reduction and the preferences of the decision maker were included in the sensitivity analysis. The results confirmed the suitability of the proposed multi-criteria evaluation approach in intelligent decision supporting requiring consideration of compensation reduction and different preferences. The results indicate the potential of FPV systems as an alternative to GMPV, especially in terms of technical performance, and encourage further research into FPV in terms of its suitability and cost-effectiveness.