For a good, seamless run along the water, a good bet is to run along the Limmat River. The best bet is to run along the river from central Zurich going north (i.e. away from the lake, downriver). There is a path most of the way, with occasional sidewalks, to Kloster Fahr (Fahr Abbey). It is 8.8 km (5.5 miles). One can run on either side of the river, although the path is a little more seamless along the eastern side. There are a few pedestrian bridge crossings along the way.
Below are some distances to key segments along the way, starting at the Zurich Marriott, next to the Dynamo Jugendkulturhaus cultural center. To go one way, it is possible to take the S3 headed back to Zurich, which runs in the western side of the river along Limmatstrasse.