Marc Richards had given the hosts an early lead but the Iron never gave up and Waterfall grabbed a point in the 88th minute.
Scunthorpe had conceded early at York in midweek and they were in trouble again when Waterfall failed to deal with a low cross in the eighth minute and Richards fired past Sam Slocombe from the edge of the box.
The visitors had a chance to level in the 29th minute but Sam Winnall hooked over from close range after a corner was headed across goal, and Chesterfield were close to a second in the 56th minute when Jamie Devitt saw a 20-yard drive tipped over.
Devitt curled a 25-yard free-kick against the crossbar four minutes later while Richards headed home a Gary Roberts cross in the 75th minute only for an offside flag to cut short his celebrations.
And Scunthorpe took advantage two minutes from time. Terry Hawkridge curled in a free-kick from the right and Waterfall was allowed to run unchallenged to head past Tommy Lee.