Contamination of water and food with cyanotoxins poses human health risks, and hence the need for sensitive early warning tools to monitor these in water. A composite of glutaraldehyde-crosslinked chitosan and multi-walled carbon nanotubes (ChMWCNTs) was synthesised and tested for potential use as a solid-phase adsorption toxin tracking (SPATT) adsorbent for monitoring microcystins (MCs) in fresh water. The composite was characterised by Fourier transform infrared spectroscopy, Brunauer–Emmett–Teller theory and scanning electron microscopy. Batch adsorption experiments to assess the effect of contact time, adsorbent dosage and initial microcystin-LR (MC-LR) concentration were conducted. The composite was found to be efficient in adsorbing MC-LR, showing 97% removal and a maximum adsorption capacity of 4.639 μg/g under optimised conditions of 5 μg/L of MC-LR, adsorbent dose of 0.03 g/5 mL and 30 min contact time. The adsorption kinetics were better explained by a pseudo-second-order model, inferring chemisorption adsorption. The isotherm data better fitted the Langmuir isotherm model, thus inferring monolayer surface adsorption. For desorption, 100% methanol was the most effective, with an efficiency of 84.71%. The composite effectively adsorbed and desorbed three congeners of MCs (–LR, –RR and –YR) when tested in raw dam water, regardless of its lower maximum adsorption capacity compared to those of other adsorbents used for similar purposes.