In this study, a gluteraldehyde-crosslinked chitosan (ChGLA) hydrogel and a glutaraldehyde-crosslinked chitosan–multiwalled carbon nanotubes composite (ChMWCNT) were synthesized to be used as substrates in the solid-phase adsorption toxin tracking (SPATT) sampling of microcystins (MCs) in irrigation water. The synthesized samplers were tested for their efficiency by deploying them in four farm dams and two canals for 48 h in January 2022 and in July 2022. Grab samples were collected during deployment and retrieval of the samplers for comparison. Sequential extraction using 100% methanol was used to extract MCs from the samplers, followed by enzyme-linked immunosorbent assay (ELISA) analysis for total MCs and liquid chromatography–mass spectrometry (LC-MS) for individual MC congeners (MC-LR, -RR, and -YR). The mean levels of dissolved total MCs detected by the samplers were as follows: ChMWCNT 0.754 (±1.085) µg g−1, ChGLA 0.420 (±0.546) µg g−1; and these were comparable to the Diaion® HP-20 resin: 0.602 (±0.627) µg g−1 of material. The mean level of MCs detected in the grab samples was 0.868 (±1.358) ug L−1. Significantly higher levels of MCs were detected in July compared to the January sampling by the two newly developed samplers. With regards to the detection of MC-LR, -RR, and -YR, no statistical differences were reported among the three samplers (ChGLA, ChMWCNT, and Diaion® HP-20) for five of the six sampling points (one-way ANOVA at a 0.05 level of significance). The levels of detection of MCs by the substrates were in the order MC-YR > -LR > -RR. Strong positive correlations between the grab samples and the ChGLA and ChMWCNT samplers suggested better suitability of the two chitosan-based sorbents for monitoring MCs in the study area compared to the Diaion® HP-20 resin. Overall, the two new sorbents showed potential for use in SPATT to monitor the presence of MCs in the agricultural waters tested, and they could represent economical and environmentally friendly options compared to the synthetic aromatic resins.