To clarify, I believe the
graphs show combined traffic, but the bandwidth meter should only show public traffic.
Does netstat show the traffic as being to port 3306 (mysql)? If not, which port?
On your database server, try something like this to monitor all TCP connections on non-private IPs with tcpdump:
Code:
$ sudo tcpdump -n -i eth0 'tcp[tcpflags] & (tcp-syn|tcp-fin) != 0 and not src and dst net 192.168.128.0/25'
tcpdump: verbose output suppressed, use -v or -vv for full protocol decode
listening on eth0, link-type EN10MB (Ethernet), capture size 96 bytes
11:40:47.694319 IP 192.0.2.103.50373 > 97.107.134.213.80: Flags [S], seq 1628722382, win 5840, options [mss 1460,sackOK,TS val 294149842 ecr 0,nop,wscale 6], length 0
11:40:47.747661 IP 97.107.134.213.80 > 192.0.2.103.50373: Flags [S.], seq 4080896205, ack 1628722383, win 5792, options [mss 1460,sackOK,TS val 381323993 ecr 294149842,nop,wscale 5], length 0
11:40:50.310730 IP 192.0.2.103.50373 > 97.107.134.213.80: Flags [F.], seq 1, ack 1, win 92, options [nop,nop,TS val 294150497 ecr 381323993], length 0
11:40:50.349323 IP 97.107.134.213.80 > 192.0.2.103.50373: Flags [F.], seq 1, ack 2, win 181, options [nop,nop,TS val 381326595 ecr 294150497], length 0
In this example, there's one connection with two start packets (the first and second -- see the [S] and [S.] flags) and two finish packets ([F.] and [F.]). This should give you an idea of what's going on. (You can also change the "and not" to "and" for traffic traversing just the private network.)
As a matter of security, you probably want to firewall traffic to your mysql server from non-trusted source IP addresses. You could consider the public IP of your web server to be non-trusted, drop any such traffic, and then see what breaks.
Also, take a look at munin, especially the ip_ plugins. By adding a passive rule to iptables, it will monitor traffic involving a particular IP address, which is a lot more granular than graphing by interface:

(I'm using two public IPs in this example, but same deal.)
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Code:
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