A novel mesoporous silica material containing boron–dipyrromethene (BODIPY) moieties (I) is employed for the detection of nerve agent simulants (NASs) and the organophosphate nerve or chemical warfare agents (CWAs) Sarin (GB), Soman (GD), and Tabun (GA) in aqueous environments. The reactive BODIPY dye with an optimum positioned hydroxyl group undergoes acylation reactions with phosph(on)ate substrates, yielding a bicyclic ring. Due to aggregation of the dyes in water, the sensitivity of the free dye in solution is very low. Only after immobilization of the BODIPY moieties into the silica substrates is aggregation inhibited and a sensitive determination of the NASs diethyl cyanophosphonate (DCNP), diethyl chlorophosphate (DCP) and diisopropyl fluorophosphate (DFP) possible. The signaling mode is a strong quenching of the fluorescence, reaching LODs in the pM range. The best performing hybrid material was singled out from a library of hybrid silicas varying in morphology and surface functionalization. The response to actual CWAs such as GB, GD, and GA has also been tested, offering similar behavior as for the simulants. The proposed reaction mechanism has been verified by investigation of other model materials, containing for instance BODIPY moieties without an optimum hydroxyl group (III) or a BODIPY dye with an all-aliphatic counterpart (IV). The latter can only form a monocyclic reaction product, showing much less reactivity as I. Assays with other possible competitors have been additionally carried out, showing favorably low cross-reactivities. Finally, the determination of NASs in several natural waters has been demonstrated.