Interconnected river system networks is a national water conservancy strategy in China and focus of research. Here we discuss the classification system, material and energy exchange between rivers and lakes, various dynamic flows and ecological functions of river-lake interconnected relationships. We then propose a novel method for the health assessment of river systems based on interconnected water system networks. In a healthy river system there is “material and energy exchange” and it is the first and foremost relationship of material and energy exchange between rivers and lakes. There are unobstructed various “flows” between rivers and lakes including material flows (water, dissolved substances, sediments, organisms and contaminants), energy flows (water levels, flow and flow velocity), information flows (information generated with water flows, organisms and human activities) and value flows (shipping, power generation, drinking and irrigation). Under the influences of nature and human activity, various flows are connected by river-lake interconnection to carry material and energy exchange between rivers and lakes to achieve river-lake interactions. The material and energy exchange between rivers and lakes become one of the approaches and the direct driving forces of changes in river-lake interconnected relationships. The benignant changes in river-lake interconnected relationship tend to be in relatively steady state and in ideal dynamic balance.