Solution 1:

C - 741 621 600 characters (but handles the new cases properly)

$ gcc water.c && ./a.out < test6.txt 
                                     __       ___    
                                    /  \xxxxx/       
                                   / _______         
                     ________     /  \     /         
               _____/        \xxx/__  \xxxx\_        
____          /               \xxxx/__/xxxxx/        
    \xxxxxxxx/                 \xxxxxxxxx/           
      \xxxxxx\                 /xxxx/                

#include<stdio.h>
char d[99][99],*p,*e,*z,*s=d,c,S=' ',D='-',O='.',U='_';n,w,x,N=99,i;
g(y){for(i=0;!i;p+=N,e+=N){i=*p==D;for(z=p;z!=e;z+=y){if(*z!=O&&*z!=
D)break;*z=*z==O?S:U;}}}f(char*n,int r){if(*n==O||*n==D){*n=r>0?'x':
S;int k;for(k=0;k<9;k++)f(n+k/3*N-N+k%3-1,r+k/3-1);}}main(){for(p=s;
gets(p);p+=N,n++){x=strlen(p)-1;w=x>w?x:w;}for(p=s,e=d[N];p<s+N;p++)
{for(i=1,z=p;z<e;z+=N)c=*z,c==0?*z=c=S:0,i?c==S?*z=O:c==U?*z=D:0:0,(
c=='/'&&z[1]!=U)||(c=='\\'&&z[-1]!=D)||c==U?i=1-i:0;}p=s;e=s+w;g(1);
p=s+w;e=s;g(-1);for(p=s;p<s+w;p++){for(z=p;*z==S;z+=N);f(z,1);}for(i
=0;i<n;i++)printf("%.*s\n",w+1,d[i]);}

Solution 2:

Ruby, 794 759 769 752 715 692 663 655 626  616

Additional test cases:   http://pastie.org/708281   and   http://pastie.org/708288   and   http://pastie.org/708310

Compressed except for indent:

def g i,j,&f
  t=[-1,0,1]
  t.each{|r|next if@w[i][j,1]=='_'&&r>0
    t.each{|c|a=i+r
      b=j+c
      if a>=0&&b>=0&&a<@r&&b<@c
        @t[a]||=[]
        if r!=0&&c!=0
          k=@w[a][j,1]
          l=@w[i][b,1]
          next if/[\/\\]/=~k+l&&((k!=l)||((r<=>0)==(c<=>0)?k!='\\': k!='/'))
        end
        e=@w[a][b,1]
        z,@t[a][b]=@t[a][b],1
        return 1if !z&&(e==' '||r>=0&&e=='_')&&yield(a,b,f)
      end}}
  nil
end
w=$stdin.readlines
@c=w.map{|e|e.size}.max-1
@w=w=w.map{|e|e.chomp.ljust@c}
z=w.map{|e|e.dup}
@r=w.size
@r.times{|r|@m=r
  @c.times{|c|e=w[r][c,1]
    z[r][c]='x'if(e==' '||e=='_')&&(@t=[]
      !g(r,c){|u,v,f|u>=@m and v==0||v==@c-1||g(u,v,&f)})&&(@t=[]
      g(r,c){|u,v,f|u==0||g(u,v,&f)})}}
puts z

Solution 3:

Python, 702 805 794 778 758 754 710 651

Handles DigitalRoss's test cases, as well as large test cases such as http://pastie.org/708764.

Example run

$ python runningwater.py < test4.txt                   
                                           ____________________________
                                          /           
                                   _      \        __
                                  / \xxxxx/       /  \
                  ___       _____/  /xxx/        /    \
____________     /   \xxxxx/   ____/xxx/ __     /xxxxxx\ 
            \xxx/    /xxxxx\__ \xxxxxx/ /xx\___/xxxxxxx/
                 ___/xxxxxxxxx\____    /xxxxxxxxxxxxxx/
                /xxxxx/      \xxxxx\__/x/    \xxxxxxx/
               /xxxxx/        \xxxxxxxx/      \xxxxx/
               \xxxxx\    _________            \xxx/
                  \xxx\  /xxxxxxxxx\           /xx/
                     \x\ \x\   /\ \x\         /xx/
    __________        \x\ \x\_/x/ /x/        /xx/
   /xxxxxxxxxx\        \x\ \xxx/ /x/        /xx/
  /xxxxxxxxxxxx\        \x\ \x/ /x/        /xx/
  \xxxxxxxxxxxxx\        \x\   /x/        /xx/
         \xxxxxxx\        \x\_/x/        /xx/
     ____/xxx/ \xx\        \xxx/        /xx/
     \xxxxxx/   \xx\___________________/xx/
      \xx/       \xxxxxxxxxxxxxxxxxxxxxxx/

Code

import sys
q=sys.stdin.readlines()
e=enumerate
s=type
k=int
o=[]
t=[0]*max(map(len,q))
n=1
L=[]
l={}
for p,d in e(q):
 w=a=0;o+=[[]]
 for i,c in e(d):
  T=t[i];C=[[c,T]];D=d[i+1:];b=0;o[-1]+=C;L+=C
  if c in'_ ':
   if('/'in D or '\\'in D)*(T%2-1)*w*p:
    for j in range(max(i-1,0),min(i+2,len(o[p-1]))):R=o[p-1][j][0];b=R*(k==s(R))or b
    for x in L:x[0]=b*(x[0]==a)or x[0]
    a=C[0][0]=b or a or n
  elif c in'\\/':w=1;a=0;n+=1
  D=d[i-1]+c;t[i-1]+=(D=='/_');t[i]+=(c in'_/\\')+(D=='_\\')
for i,a in e(o):
 for c,r in a:
  if(r==0)*(s(c)==k):l[c]=1
 for j,(c,r)in e(a):
  if(c in l)-1:a[j]=q[i][j],0
 print''.join((k==s(x))*'x'or x for x,r in a),

Solution 4:

Perl, 534 545 550 566 569 567 578 594 596

sub i{$a=1;$a^=substr(x.$l[$_],$_[0],3)=~/^(.[_y]|.\/[^_]|[^_]\\)/for 0..$r-1;
$a}sub f{$c=$e-$s;$_=$l[$r];$f=s/(.{$s})(.{0,$c})/$1<$2>/;(/[ _x]>/&i$e-1and$f=
/>[ _xy]*[\\\/]/,$e=$+[0]-2)or/[ _]*>/,$e=$-[0]-1;(/<[ _x]/&i$s and$f&=
/[\\\/][ _xy]*</,$s=$-[0])or/<[ _]*/,$s=$+[0]-1;$f&$s<$e&&substr($l[$r],$s,$e-$s
)=~s!([\\/][ _xy]*)([\\/][ _]*)!($t=$1)=~y/ _/xy/,$t.$2!eg,$r--&&&f}$q=@l=<>;
while($q--){i$-[0]+1and substr($l[$r--],$-[1],length$1)=~y/_y/x/,$s=$-[0],$e=
$+[0],$q&&f while$l[$r=$q]=~m~\\/|[\\/]([_y]+)[\\/]~g}y/y/x/,print for@l

This handles all the test cases that I've seen. Newlines are optional and are only there for formatting.

Call it as e.g. perl water.pl test.txt.

Here's another funny edge case (for my algorithm anyway) not in any of the previous examples:

__      _
  \__  /
    /_/

The verbose version I'd put up earlier still fails on that.