Sampling water from shallow estuaries, rivers, or lakes, particularly where access is difficult, can be problematic. In estuaries at low tide, water depths can be less than a meter, and therefore conventional samplers based on vertical tubes of plastic or metal, such as Nansen and Niskin bottles, are inappropriate. During three consecutive years (2017–2019) whilst studying eutrophication in the shallow waters of the marginal Estero Salado (ES, Gulf of Guayaquil, Ecuador), a range of tubular water samplers were designed, constructed, and tested. Six of these designs are presented here and all use inexpensive recyclable and locally available materials. The sampling bottles were mainly made from readily available plastic components, including non-returnable drinking water bottles, acrylic/PVC pipes, tweezers, elastic bands, discarded gym weight plates, and closures made from plumbing items. Up to 80% of the materials used were recyclable. Costs ranged from 5 to 35 US$, and the time to design and construct was up to two days. The horizontal sampling bottles proved strong enough for rigorous field conditions. Sampling at depths <1 m, the bottles did not show any sign of collapsing due to either the hydrostatic pressure when empty nor the weight of the water sample. Three samplers are submerged with open ends to the depth required, and then moved sideways or allowed to align with the current to flush the interior. Then, a messenger or pulling on a line closes the bottle. A simple tap or direct dispensing is used to transfer the water into storage bottles. Two of the designs (with one end open) can be used to sample right through the very surface layer. Two of the designs that enter the water with closed ends were inter-compared with a standard Niskin water sampler and gave statistically comparable results. The lightest sampler was tested at various depths down to 5 m in a lake with no operational issues, and nutrient data from samples gave a coherent vertical profile. Two of the designs (with one end open) can be used to sample the very surface layer. The water samplers reported here are highly appropriate for laboratories with very limited resources and can be used in very shallow waters under a wide range of environmental conditions. Results from samples collected with the described samplers show that the inner estuarine branches of the ES are now under perennial hypoxic, acidic, and hypereutrophic conditions with extremely high total and fecal coliform loads.