The development, proposed for land off Canal Way in the town, would back on to the Llangollen Canal that runs past Ellesmere.
Developer Burbury Investments says it will put in flood mitigation works because the area has the potential to flood.
In a letter to Shropshire Council, The Canal and River Trust says it wants more details of the flood compensation area.
"The proposal indicates flood compensation works in close proximity to the canal and the trust needs to be satisfied that this work will have no adverse impact on the structural integrity of the canal," the letter says.
The trust also wants to know whether any surface water will be discharged into the canal, saying this could affect the water quality and bio diversity.
"There are no details of how the canal and its users will be protected from dust and noise during construction or how silt or any run-off will be managed," it adds.
The trust has also offered to work with developers to look at how canal water could be used in cooling and heating on the development.
In its planning application documents, the developer says that land within the overall scheme, close to the canal, has been earmarked for special storage areas for potential flood water.
The report says: "This first phase of residential development is being brought forward in advance of the wider flood risk management scheme.
"Therefore, a standalone solution is proposed which will mitigate flood risk to the phase one development without conflicting or impeding the implementation of the future de-culverting of the Tetchill Brook and floodplain consolidation works."
The homes would be part of a larger development that proposes hotel and pub, log cabins and a touring caravan site.