Some are lingering scars, like the bullet holes in city buildings. Other effects are ongoing, like the unexploded land mines that still dot Croatia's countryside.
Up to two million mines were laid by both the Croatians and Serbians during the war, leaving the country with one of the worst land mine problems in Europe.
The Croatian Mine Action Centre (CROMAC) reports there are around 9 counties and 60 towns still contaminated with approximately 40,000 unexploded mines - it's estimated that land mine clearing efforts will continue until at least 2019.
Mines were mostly laid in inland rural areas along the front lines. The worst affected areas were Eastern Slavonia, Brodsko-Posavska County, Karlovac County, areas around Zadar and more remote areas of the Plitvice Lakes National Park. Suspected minefields are typically found in woodlands, forests, agricultural land, meadows and pastures. As a result of this ever present danger in Croatia, there are 13,498 warning signs across the country.
Hundreds of people were killed by land mines during and immediately after the war but this number has rapidly decreased in recent years.
There is some debate online about the number of casualties among tourists and the accuracy of these figures given the potential impact on tourism, however there's no doubt the number is very small.
A Dutch tourist lost a leg in 2003 after stepping on a mine on the island of Vis, but it's believed he had crossed a warning sign on an old army base.
For most travellers, the risk presented by land mines is minimal - this is Croatia, not Call of Duty.
If you stick to the main towns and cities along the coast you're no more likely to encounter a land mine than you are walking down the main street of your home town.
According to CROMAC, the road network, tourist destinations, public facilities and other commonly used areas have all been declared secure.
However, adventure tourism is becoming more and more popular in Croatia, and many of these activities take place away from the main tourist centres.
If you plan to get off the beaten track, it pays to do some research beforehand.
Before you head off to master the rapids or tear up the countryside on your mountain bike, check the CROMAC website for updated maps of known and suspected mine areas. The website also lists all of their regional offices which can provide more specific information on the affected areas.
Once you get there, it may be tempting to get in touch with your wild side but you should stick to known safe roads when driving and marked paths when hiking or mountain biking.
The decreased casualty rate from land mines in Croatia is thanks to an ongoing campaign to map out and signpost minefields.
However, remember that tourism is still a growing industry in Croatia, so unlike other European countries where English is an unofficial second language, not every sign or warning is translated.
Most minefields are marked with rectangular white signs reading "Ne prilazite - na ovom podrucju je velika opasnost od mina". This roughly translates to "Do not cross - there are landmines in the area".
Don't worry if you haven't brushed up on your Croatian or have left your phrasebook at the hostel - these signs also feature the international symbol for land mines, a red triangle featuring a skull and crossbones.
Even though you might fancy yourself as the next Indiana Jones, if you're out and about in the countryside many guides recommend staying away from abandoned houses, especially those that look like shells have hit them, as there may be more unexploded mines nearby.
White water warriors should also watch where they strap on their life jackets.
The Zrmanja River in northern Dalmatia, and Mreznica River in Karlovac County, are popular spots for canoeing and raft trips, but the banks and surrounding land can present mine risks.
In fact some areas around the Mreznica River are completely inaccessible because of minefields.
If you're unsure, you can join an organised tour with a local guide who knows where - and where not - to go.
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