From your meagre description of the files, I assume that each files data is keyed by date & time?

If so, the rather than loading all the data into arrays, accumulate it in a hash:

my %data;
open FILE, '<', 'gravity' or die;
while( <FILE> ) {
    my @fields = split ' ', $_;
    $data{ @fields[ 0, 1 ] } = join "\t", @fields;
}
close FILE;

open FILE, '<', 'magnetics' or die;
while( <FILE> ) {
    my @fields = split ' ', $_;

    ## Pad the hash if we didn't see this date/time in the gravity fil
+e
    $data[ "@fields[ 0, 1 ]" } //= join "\t", @fields[ 0,1 ], ('n/a') 
+x 3; 

    $data{ "@fields[ 0, 1 ]" } .= join "\t", @fields[ 2 .. $#fields ];
}
close FILE;

open FILE, '<', 'bathymetry' or die;
while( <FILE> ) {
    my @fields = split ' ', $_;

## Pad the hash if we didn't see this date/time before (How many field
+s added by the magnetics?)
    $data[ "@fields[ 0, 1 ]" } //= join "\t", @fields[ 0,1 ], ('n/a') 
+x ???;

    $data{ "@fields[ 0, 1 ]" } .= join "\t", @fields[ 2 .. $#fields ];
}
close FILE;

for my $key ( sort keys %data ) {
    print $data{ $key };
}
[download]

Depending upon your date & time formats, you might need a more sophisticated sort.