A sampler was needed for a spatial and temporal study of microbial and chemical stratification in a large swine manure lagoon that was known to contain zoonotic bacteria. Conventional samplers were limited to collections of surface water samples near the bank or required a manned boat. A new sampler was developed to allow simultaneous collection of multiple samples at different depths, up to 2.3 m, without a manned boat. The sampler was tethered for stability, used remote control (RC) for sample collection, and accommodated rapid replacement of sterile tubing modules and sample containers. The sampler comprised a PVC pontoon with acrylic deck and watertight enclosures, for a 12 VDC gearmotor, to operate the collection module, and vacuum system, to draw samples into reusable autoclavable tubing and 250-mL bottles. Although designed primarily for water samples, the sampler was easily modified to collect sludge. The sampler held a stable position during deployment, created minimal disturbance in the water column, and was readily cleaned and sanitized for transport. The sampler was field tested initially in a shallow fresh water lake and subsequently in a swine manure treatment lagoon. Analyses of water samples from the lagoon tests showed that chemical and bacterial levels, pH, and EC did not differ between 0.04, 0.47, and 1.0 m depths, but some chemical and bacterial levels differed between winter and spring collections. These results demonstrated the utility of the sampler and suggested that future manure lagoon studies employ fewer or different depths and more sampling dates.