I have QGIS 2.8.2 Wien on windows 7 and quite new to QGIS. I have two shapefiles - 1 with rivers and 2 with sites located on some of those rivers. I want to carry out a spatial query to find the river sections that have sites located on them, but when I carry out the query, no sections are found, although there should be over 100 of them. I have checked that the CRS is the same on both layers (EPSG:29903 TM75 Irish grid), I don't know why results don't show up.
Use Processing toolbox > select by location and choose intersects and choose a precision of 50 meters (or whatever buffer you think is appropriate.) Alternatively you could buffer the rivers with a 50m buffer (again or whatever is appropriate) then do a select by location of the points to the polygons and this time select within instead of intersects. This will select all points of interest that are on or near the river. Then export these set of points out and you are ready to go.
Maybe some geometries are not valid, can you check their validity with "Check Geometry Validity" Tool ?
If it's a validy problem, you can then fix them : Fixing geometry validity errors in QGIS?