While I am using the browser I often hear the external HDD spin up. This causes the browser to freeze for about 5 - 10 seconds while the drive is doing whatever it is doing. I am not sure why this is happening or how I can go about resolving the issue, but how can I make this behavior stop? It wasn't always like this.
I have a similar experience, sometimes multiple back-to-back spin-ups of an external drive used only for Time Machine and excluded --to the best of my ability-- from indexing. I ran lsof filtered for the drive name and got this result:
COMMAND PID USER FD TYPE DEVICE SIZE/OFF NODE NAME
Finder 297 henry 19r DIR 14,6 204 92 /Volumes/Time Machine Backups/Backups.backupdb
(Headers added manually. This may not format well here, sorry.) This seems to be repeatable for spinups clearly not related to actual Time Machine backups. Near as I can tell the Finder is reading the top level directory for Time Machine files on that drive. What could it be looking for? The most likely, to my mind, perhaps the only useful data: last-modified time stamps. Of the files in that directory, there are only two I see that are contemporary:
"Charley" is my host name. It is Finder and not Time Machine asking. (Time Machine most certainly can retain internally the time of its last actual backup.) Why would Finder need to know? The only possibility I can think of is that Finder is asking if that directory tree has been modified so it might rebuild Spotlight indexes if necessary. Maybe I have not completely disabled indexing for that drive. Or, even with indexing disabled, Finder still monitors the drive for changes, even though it won't index even if a change has occurred. The next mystery: what triggers these checks? Does it mean anything that they occur, sometimes one-after-another? Superstitiously, these all appear while I am browsing, primarily in Firefox (current version). Is Firefox tickling Finder somehow?
Hope this evidence helps.
A process is accessing the drive, thus it spins up. To identify what process is accessing the drive, wait for it to spin up in the manner you described, then jump into Terminal and enter this command:
lsof | grep /Volumes/NameOfVolume
This will list the file or files on the drive being accessed, and the service accessing them.