Fluoroquinolone antibiotics (FQs) are ubiquitous and ionisable in surface waters. Here we investigate gatifloxacin (GAT) and balofloxacin (BAL), two widely used FQs, and determine the photochemical reactivity of their respective dissociation species that arise at different pH to understand the relevance and pathways of phototransformation reactions. Simulated-sunlight experiments and matrix calculations showed that neutral forms (HFQs0) of the two antibiotics had the highest apparent photolytic efficiency and hydroxyl-radical oxidation reactivity. Based on the pH-dependent photochemical reactivities, the solar apparent photodegradation half-lives (t1/2) in sunlit surface waters ranged from 14.5–169 min and was 1–2 orders of magnitude faster than hydroxyl-radical induced oxidation (t1/2 = 20.9–29.8 h). The corresponding pathways were proposed based on the identification of key intermediates using HPLC-ESI-MS/MS. The apparent photodegradation induced defluorination, decarboxylation, and piperazinyl oxidation and rearrangement, whereas hydroxyl-radical oxidation caused hydroxylated defluorination and piperazinyl hydroxylation. The photomodified toxicity of GAT and BAL was examined using an Escherichia coli activity assay. E. coli activity was not affected by BAL, but was significantly affected by the photo-modified solutions of GAT, indicating that primary photo-degradates have a comparable or higher antibacterial activity than the parent GAT. In fresh water and seawater this antibacterial activity remained high for up to 24 h, even after GAT had undergone significant photodegradation (>1 half-life), indicating the potential impact of this chemical on microbial communities in aquatic systems.