Sulfite-based photocatalysis has been recently employed as a promising technology for the treatment of organic pollutants via the generation of reactive radicals. In this contribution, the effect of wastewater matrix constituents and toxicity evaluation were systematically investigated in the FeIII impregnated N-doped TiO2 (FeN-TiO2)/sulfite/visible LED (Vis LED) process in the presence of diphenamid (DPA) as a model organic pollutant. The results showed that the presence of HCO3-, SO42-, NO3-, and F- had no detrimental effect on DPA degradation. Conversely, the presence of Cr(VI), NO2-, Cl-, and Br- caused a stronger retardation effect. The effect of natural organic matter such as humic acid (HA) was inert at normal concentrations. Interestingly, the retardation effect of inorganic ions can be quantified at any given ion concentration based on the linear correlations between the DPA decay (first-order kinetic constants) and concentration of ion species. Toxicity tests on Synechocystis sp., Microcystis flos-aquae, and Nostoc sp. algae revealed that higher toxicity was noticed at 240 min treatment time accompanied by lower toxicity with prolonging the treatment time for all selected algae except for Microcystis flos-aquae. In addition, novel two-phase mathematical models were successfully proposed to predict the accumulation of intermediates depending on their evolution profile.