my $n = 3;
my $newword = NEW;
my $n_minus_one = $n-1;
while (<DATA>) {
    s/((?:\w+\s+){$n_minus_one})(\w+)/$1$newword/;
    print;
}    

__DATA__
hi there everyone I am looking to substitute
lots of words for new ones, but only the third
word per line on each line!
one
one two
one two three
one two three four
__OUTPUT__
hi there NEW I am looking to substitute
lots of NEW for new ones, but only the third
word per NEW on each line!
one
one two
one two NEW
one two NEW four
[download]

update - Now that I think about some edge cases like apostrophes and hyphens I would change line to

s/((?:\w+\s+){$n_minus_one})(\w+)/$1$newword/;
[download]

to

s/((?:[\w'\-]+[^\w'\-]+){$n_minus_one})(\w+)/$1$newword/;
[download]

--

flounder