Abstract: Linear features of the waterbodies of waterways or rivers make it hard to bypass construction projects associated with waterways in nature reserves. Actually, all the construction projects, such as inland transport waterways, crossing bridges, and flood control installations in related regions, are confronted more or less with some legal barriers. Conservation and rational exploitation of the water bodies of rivers or waterways are paradoxes hard to be taken care of simultaneously. From the angle of promoting harmonized development of conservation of aquatic organism diversity, eco-social construction and people’s livelihood on the banks of these rivers, analysis was done of such problemsissues as failure of the “Regulations for Nature Reserves in China" concerning environmental permission for construction projects alongside the rivers or waterways in the reserves to take into account specificities of these waterbodies; inapplicability of the rules for functional zoning of nature reserves to those of the waterway type; and lack of rules concerning nature reserves in the river or waterway related laws. On such a basis, some countermeasures are proposed, e.g. permissions should be granted conditionally to some capital construction and liveliness projects in the buffer zones and core zones of nature reserves; the environmental permission system should be further consummated; and environmental management of the construction projects within river or waterway type nature reserves should be intensified, etc..