I've been in Venice recently in mid May and mid/late October. Temperatures both times were rather pleasant - not too cold, not too hot. Around 20-24C by afternoon. I don't think it got much below 12-15C the 5 nights were were there last October. No floods either but the gang planks are available and ready for deployment all the time. Mostly summer wear for us but we did have a pullover for ferry rides to the outlying islands. I do seem to remember there was evidence of recent flooding- at least seaweed washed over the quays - after we got there.

Maybe keep an eye on the tide table coefficients (if offered) when you plan to visit. 100 appears to be the benchmark for past historic tidal highs but Atlantic France is getting coefficients of 115 or even more some days. Med tides seem to be a lot-less variable than Atlantic tides but every little bit makes a difference for Venice.

My wife and I also go to Austria often (she has relatives there) and were where you plan to go (Vienna, Salzburg, Innsbruck) in mid October 2012 and 2013. Weather again is rather pleasant. I would say not cool/cold at all. We've had some scorching early springs (32C+ by 10am).

Check out this tidetable link for your dates there. The tide coefficient was high 90s the 2 days before we got there which would explain the evidence of recent flooding.