Heads up nut flush with ugly river

Opponent and i just started playing, no real reads but he doesnt seem to be the typcial "all-in donk" that you often see at these levels, then again we have played maybe 10 hands. $50 NL equal stacks this is an actual heads up game and not a 6-max or ring game between the blinds

Villan: Posts BB of $.50
Hero: Posts SB of $.25
Hero: K [img]/images/graemlins/heart.gif[/img]Q [img]/images/graemlins/heart.gif[/img]
Hero: raises to $1.75
Villan Calls

Flop: A [img]/images/graemlins/club.gif[/img] 4 [img]/images/graemlins/heart.gif[/img] 9 [img]/images/graemlins/heart.gif[/img]
Villan: Checks
Hero: Bets $3
Villan: calls

Turn: 10 [img]/images/graemlins/heart.gif[/img]
Villan: Checks
Hero: bets $9
Villan: calls

River: A [img]/images/graemlins/spade.gif[/img]
Villan: Pushes all in
Hero: ???

Ok so its pretty obvious that villan has an A, what I was putting him on the entire hand, but does he just have a set here enough of the time to justify the call? Comments on all streets appreciated.